القائمة
Compare gene signatures across perturbations and suggest clustering or grouping.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
Manage the BioAPEX current-feature workflow from scoping through review and completion
Turn an analysis request into a Slurm-ready execution plan with commands, resource assumptions, and job structure.
Scale a buffer recipe to a target volume and compute component masses/volumes.
Save a fetched summary or document to the knowledge base for later retrieval (e.g. after PubMed/UniProt lookup).
Interpret scRNA clusters using marker genes and suggest cell type or state.
Critically evaluate a perturbation hypothesis — challenge assumptions, propose negative controls, and flag confounders.
| name | perturbation_signature_compare |
| description | Compare gene signatures across perturbations and suggest clustering or grouping. |
| category | bio/perturb_seq |
| version | 1 |
| requires_tools | ["read_file","python_repl"] |
| requires_network | false |
| user_invocable | true |
| species | any |
| modality | perturb_seq |
| stage | analysis |
| stability | experimental |
| safety_level | low |
User has multiple perturbation signatures (e.g. DE lists or effect sizes per gene per perturbation) and wants to compare or group them.
Load: If paths given, use read_file; otherwise ask for a matrix or list of (perturbation, gene, score) triples.
Structure: Build a perturbation × gene matrix (e.g. log2FC or binary DE).
Compare: Use python_repl to compute:
Cluster: Suggest grouping (e.g. "perturbations A and B are similar; C is distinct") and optionally suggest visualization (heatmap, dendrogram).
Summarize: Table or list of similar pairs/groups and one-sentence biological interpretation.
